Starting phenix.real_space_refine on Sun Sep 29 07:45:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/09_2024/7mil_23855.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/09_2024/7mil_23855.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/09_2024/7mil_23855.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/09_2024/7mil_23855.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/09_2024/7mil_23855.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mil_23855/09_2024/7mil_23855.cif" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 132 5.16 5 Na 1 4.78 5 C 14168 2.51 5 N 3552 2.21 5 O 3892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 21753 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5347 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 18, 'TRANS': 637} Chain breaks: 1 Chain: "B" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5347 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 18, 'TRANS': 637} Chain breaks: 1 Chain: "C" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5347 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 18, 'TRANS': 637} Chain breaks: 1 Chain: "D" Number of atoms: 5347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5347 Classifications: {'peptide': 656} Link IDs: {'PTRANS': 18, 'TRANS': 637} Chain breaks: 1 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 92 Unusual residues: {' NA': 1, 'POV': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'POV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 12.63, per 1000 atoms: 0.58 Number of scatterers: 21753 At special positions: 0 Unit cell: (141.57, 139.854, 126.126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 132 16.00 P 8 15.00 Na 1 11.00 O 3892 8.00 N 3552 7.00 C 14168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.04 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.04 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.04 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.04 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.14 Conformation dependent library (CDL) restraints added in 2.9 seconds 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 8 sheets defined 63.0% alpha, 2.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'A' and resid 114 through 130 removed outlier: 4.112A pdb=" N LYS A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG A 122 " --> pdb=" O ARG A 118 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 126 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 146 removed outlier: 3.838A pdb=" N LEU A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 140 " --> pdb=" O ARG A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 163 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.844A pdb=" N LYS A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.572A pdb=" N ILE A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 205 removed outlier: 3.856A pdb=" N ASN A 205 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 removed outlier: 3.759A pdb=" N ILE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 238 removed outlier: 3.610A pdb=" N THR A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.606A pdb=" N THR A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 283 removed outlier: 4.087A pdb=" N VAL A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN A 279 " --> pdb=" O PRO A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.799A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.709A pdb=" N MET A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 321 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'A' and resid 345 through 352 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.813A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.571A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 434 removed outlier: 3.650A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A 434 " --> pdb=" O HIS A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 461 removed outlier: 3.683A pdb=" N MET A 440 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR A 454 " --> pdb=" O PHE A 450 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 458 " --> pdb=" O THR A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 507 removed outlier: 3.928A pdb=" N LEU A 491 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 492 " --> pdb=" O MET A 488 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 removed outlier: 3.774A pdb=" N GLN A 514 " --> pdb=" O SER A 511 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 515 " --> pdb=" O ASP A 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 511 through 515' Processing helix chain 'A' and resid 521 through 542 removed outlier: 3.547A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL A 528 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 541 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE A 542 " --> pdb=" O PHE A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 4.112A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 569 removed outlier: 3.558A pdb=" N TYR A 565 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 566 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG A 567 " --> pdb=" O TYR A 564 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY A 568 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 569 " --> pdb=" O THR A 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 569' Processing helix chain 'A' and resid 572 through 584 removed outlier: 3.849A pdb=" N SER A 576 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 577 " --> pdb=" O GLY A 573 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU A 584 " --> pdb=" O GLN A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 607 removed outlier: 4.089A pdb=" N PHE A 592 " --> pdb=" O LEU A 588 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.996A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 removed outlier: 3.790A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 686 removed outlier: 3.644A pdb=" N ILE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 675 " --> pdb=" O ASN A 671 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 706 removed outlier: 3.668A pdb=" N ILE A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 693 " --> pdb=" O GLU A 689 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 694 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 699 " --> pdb=" O GLN A 695 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE A 703 " --> pdb=" O THR A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.663A pdb=" N PHE A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 751 removed outlier: 4.005A pdb=" N THR A 744 " --> pdb=" O THR A 740 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 749 " --> pdb=" O HIS A 745 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN A 750 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 130 removed outlier: 4.113A pdb=" N LYS B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA B 126 " --> pdb=" O ARG B 122 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 128 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 146 removed outlier: 3.839A pdb=" N LEU B 135 " --> pdb=" O CYS B 131 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG B 136 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 163 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.844A pdb=" N LYS B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 197 removed outlier: 3.572A pdb=" N ILE B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 removed outlier: 3.856A pdb=" N ASN B 205 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.759A pdb=" N ILE B 221 " --> pdb=" O THR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.611A pdb=" N THR B 231 " --> pdb=" O GLN B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.606A pdb=" N THR B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 283 removed outlier: 4.087A pdb=" N VAL B 278 " --> pdb=" O GLN B 274 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN B 279 " --> pdb=" O PRO B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.800A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.710A pdb=" N MET B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR B 321 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE B 324 " --> pdb=" O MET B 320 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 336 Processing helix chain 'B' and resid 345 through 352 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.812A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.572A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 434 removed outlier: 3.649A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 429 " --> pdb=" O LEU B 425 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 434 " --> pdb=" O HIS B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 461 removed outlier: 3.683A pdb=" N MET B 440 " --> pdb=" O PHE B 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 454 " --> pdb=" O PHE B 450 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 507 removed outlier: 3.927A pdb=" N LEU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE B 492 " --> pdb=" O MET B 488 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE B 506 " --> pdb=" O GLY B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 removed outlier: 3.773A pdb=" N GLN B 514 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 515 " --> pdb=" O ASP B 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 511 through 515' Processing helix chain 'B' and resid 521 through 542 removed outlier: 3.546A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N PHE B 527 " --> pdb=" O HIS B 523 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL B 528 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR B 540 " --> pdb=" O SER B 536 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 541 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE B 542 " --> pdb=" O PHE B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 4.112A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 569 removed outlier: 3.558A pdb=" N TYR B 565 " --> pdb=" O MET B 562 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 566 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 567 " --> pdb=" O TYR B 564 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY B 568 " --> pdb=" O TYR B 565 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE B 569 " --> pdb=" O THR B 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 562 through 569' Processing helix chain 'B' and resid 572 through 584 removed outlier: 3.850A pdb=" N SER B 576 " --> pdb=" O MET B 572 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL B 577 " --> pdb=" O GLY B 573 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 607 removed outlier: 4.089A pdb=" N PHE B 592 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.997A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 666 removed outlier: 3.790A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 686 removed outlier: 3.643A pdb=" N ILE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 675 " --> pdb=" O ASN B 671 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 683 " --> pdb=" O GLU B 679 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 706 removed outlier: 3.668A pdb=" N ILE B 691 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG B 693 " --> pdb=" O GLU B 689 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 694 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 699 " --> pdb=" O GLN B 695 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 703 " --> pdb=" O THR B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 removed outlier: 3.663A pdb=" N PHE B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 751 removed outlier: 4.005A pdb=" N THR B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 749 " --> pdb=" O HIS B 745 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN B 750 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU B 751 " --> pdb=" O SER B 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 130 removed outlier: 4.112A pdb=" N LYS C 121 " --> pdb=" O LYS C 117 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG C 122 " --> pdb=" O ARG C 118 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 126 " --> pdb=" O ARG C 122 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER C 128 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 146 removed outlier: 3.838A pdb=" N LEU C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU C 137 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN C 140 " --> pdb=" O ARG C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 163 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.844A pdb=" N LYS C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.572A pdb=" N ILE C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 205 removed outlier: 3.857A pdb=" N ASN C 205 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.758A pdb=" N ILE C 221 " --> pdb=" O THR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 238 removed outlier: 3.610A pdb=" N THR C 231 " --> pdb=" O GLN C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.606A pdb=" N THR C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 283 removed outlier: 4.087A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN C 279 " --> pdb=" O PRO C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.798A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 304 " --> pdb=" O LEU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.711A pdb=" N MET C 320 " --> pdb=" O PHE C 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR C 321 " --> pdb=" O VAL C 317 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE C 324 " --> pdb=" O MET C 320 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 336 Processing helix chain 'C' and resid 345 through 352 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.813A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.572A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 434 removed outlier: 3.650A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 429 " --> pdb=" O LEU C 425 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS C 434 " --> pdb=" O HIS C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 461 removed outlier: 3.683A pdb=" N MET C 440 " --> pdb=" O PHE C 436 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN C 452 " --> pdb=" O TYR C 448 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR C 454 " --> pdb=" O PHE C 450 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 458 " --> pdb=" O THR C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 507 removed outlier: 3.927A pdb=" N LEU C 491 " --> pdb=" O ARG C 487 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE C 506 " --> pdb=" O GLY C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 removed outlier: 3.773A pdb=" N GLN C 514 " --> pdb=" O SER C 511 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER C 515 " --> pdb=" O ASP C 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 511 through 515' Processing helix chain 'C' and resid 521 through 542 removed outlier: 3.547A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE C 527 " --> pdb=" O HIS C 523 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 528 " --> pdb=" O PHE C 524 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 534 " --> pdb=" O ALA C 530 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 540 " --> pdb=" O SER C 536 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 541 " --> pdb=" O VAL C 537 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE C 542 " --> pdb=" O PHE C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 561 removed outlier: 4.112A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 569 removed outlier: 3.559A pdb=" N TYR C 565 " --> pdb=" O MET C 562 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 566 " --> pdb=" O LEU C 563 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 567 " --> pdb=" O TYR C 564 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY C 568 " --> pdb=" O TYR C 565 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 569 " --> pdb=" O THR C 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 562 through 569' Processing helix chain 'C' and resid 572 through 584 removed outlier: 3.850A pdb=" N SER C 576 " --> pdb=" O MET C 572 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 584 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 607 removed outlier: 4.090A pdb=" N PHE C 592 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE C 595 " --> pdb=" O LEU C 591 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.997A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 666 removed outlier: 3.790A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 686 removed outlier: 3.644A pdb=" N ILE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA C 675 " --> pdb=" O ASN C 671 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN C 683 " --> pdb=" O GLU C 679 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 706 removed outlier: 3.668A pdb=" N ILE C 691 " --> pdb=" O GLU C 687 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG C 693 " --> pdb=" O GLU C 689 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU C 694 " --> pdb=" O ARG C 690 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR C 699 " --> pdb=" O GLN C 695 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE C 703 " --> pdb=" O THR C 699 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 removed outlier: 3.662A pdb=" N PHE C 715 " --> pdb=" O LEU C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 751 removed outlier: 4.005A pdb=" N THR C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU C 749 " --> pdb=" O HIS C 745 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN C 750 " --> pdb=" O VAL C 746 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 130 removed outlier: 4.112A pdb=" N LYS D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ARG D 122 " --> pdb=" O ARG D 118 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 126 " --> pdb=" O ARG D 122 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER D 128 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 146 removed outlier: 3.839A pdb=" N LEU D 135 " --> pdb=" O CYS D 131 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 137 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN D 140 " --> pdb=" O ARG D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 163 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.844A pdb=" N LYS D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.573A pdb=" N ILE D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 205 removed outlier: 3.856A pdb=" N ASN D 205 " --> pdb=" O ASP D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 225 removed outlier: 3.758A pdb=" N ILE D 221 " --> pdb=" O THR D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 238 removed outlier: 3.610A pdb=" N THR D 231 " --> pdb=" O GLN D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.606A pdb=" N THR D 272 " --> pdb=" O LEU D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 283 removed outlier: 4.087A pdb=" N VAL D 278 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN D 279 " --> pdb=" O PRO D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.800A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 303 " --> pdb=" O ILE D 299 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 304 " --> pdb=" O LEU D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.710A pdb=" N MET D 320 " --> pdb=" O PHE D 316 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR D 321 " --> pdb=" O VAL D 317 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE D 324 " --> pdb=" O MET D 320 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 345 through 352 Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 404 through 410 removed outlier: 3.813A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.571A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 422 through 434 removed outlier: 3.649A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 429 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS D 434 " --> pdb=" O HIS D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 461 removed outlier: 3.683A pdb=" N MET D 440 " --> pdb=" O PHE D 436 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN D 452 " --> pdb=" O TYR D 448 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR D 454 " --> pdb=" O PHE D 450 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL D 458 " --> pdb=" O THR D 454 " (cutoff:3.500A) Processing helix chain 'D' and resid 486 through 507 removed outlier: 3.926A pdb=" N LEU D 491 " --> pdb=" O ARG D 487 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE D 492 " --> pdb=" O MET D 488 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE D 506 " --> pdb=" O GLY D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 removed outlier: 3.774A pdb=" N GLN D 514 " --> pdb=" O SER D 511 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER D 515 " --> pdb=" O ASP D 512 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 511 through 515' Processing helix chain 'D' and resid 521 through 542 removed outlier: 3.547A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE D 527 " --> pdb=" O HIS D 523 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 528 " --> pdb=" O PHE D 524 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE D 534 " --> pdb=" O ALA D 530 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR D 540 " --> pdb=" O SER D 536 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 541 " --> pdb=" O VAL D 537 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N PHE D 542 " --> pdb=" O PHE D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 561 removed outlier: 4.112A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 569 removed outlier: 3.559A pdb=" N TYR D 565 " --> pdb=" O MET D 562 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 566 " --> pdb=" O LEU D 563 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG D 567 " --> pdb=" O TYR D 564 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY D 568 " --> pdb=" O TYR D 565 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE D 569 " --> pdb=" O THR D 566 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 562 through 569' Processing helix chain 'D' and resid 572 through 584 removed outlier: 3.849A pdb=" N SER D 576 " --> pdb=" O MET D 572 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU D 584 " --> pdb=" O GLN D 580 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 607 removed outlier: 4.090A pdb=" N PHE D 592 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE D 595 " --> pdb=" O LEU D 591 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.996A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 666 removed outlier: 3.790A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 686 removed outlier: 3.643A pdb=" N ILE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 675 " --> pdb=" O ASN D 671 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU D 679 " --> pdb=" O ALA D 675 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR D 680 " --> pdb=" O LEU D 676 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D 683 " --> pdb=" O GLU D 679 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 706 removed outlier: 3.668A pdb=" N ILE D 691 " --> pdb=" O GLU D 687 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG D 693 " --> pdb=" O GLU D 689 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 694 " --> pdb=" O ARG D 690 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR D 699 " --> pdb=" O GLN D 695 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 703 " --> pdb=" O THR D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 removed outlier: 3.662A pdb=" N PHE D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 751 removed outlier: 4.006A pdb=" N THR D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU D 749 " --> pdb=" O HIS D 745 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASN D 750 " --> pdb=" O VAL D 746 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU D 751 " --> pdb=" O SER D 747 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 73 through 74 removed outlier: 3.862A pdb=" N ARG A 73 " --> pdb=" O LYS B 722 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU B 719 " --> pdb=" O CYS B 731 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 382 removed outlier: 5.788A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 729 through 731 removed outlier: 3.571A pdb=" N GLU A 719 " --> pdb=" O CYS A 731 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 73 " --> pdb=" O LYS A 722 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 73 through 74 removed outlier: 3.909A pdb=" N ARG B 73 " --> pdb=" O LYS C 722 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS C 722 " --> pdb=" O ARG B 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU C 719 " --> pdb=" O CYS C 731 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 376 through 382 removed outlier: 5.789A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 73 through 74 removed outlier: 3.571A pdb=" N GLU D 719 " --> pdb=" O CYS D 731 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 376 through 382 removed outlier: 5.789A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 376 through 382 removed outlier: 5.790A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) 780 hydrogen bonds defined for protein. 2313 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 6.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3452 1.31 - 1.44: 5928 1.44 - 1.56: 12588 1.56 - 1.69: 20 1.69 - 1.82: 216 Bond restraints: 22204 Sorted by residual: bond pdb=" C21 POV B 902 " pdb=" O21 POV B 902 " ideal model delta sigma weight residual 1.330 1.420 -0.090 2.00e-02 2.50e+03 2.01e+01 bond pdb=" C21 POV A 902 " pdb=" O21 POV A 902 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" C21 POV C 902 " pdb=" O21 POV C 902 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C21 POV D 902 " pdb=" O21 POV D 902 " ideal model delta sigma weight residual 1.330 1.419 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C21 POV D 901 " pdb=" O21 POV D 901 " ideal model delta sigma weight residual 1.330 1.418 -0.088 2.00e-02 2.50e+03 1.92e+01 ... (remaining 22199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.89: 29579 3.89 - 7.79: 317 7.79 - 11.68: 55 11.68 - 15.57: 13 15.57 - 19.47: 4 Bond angle restraints: 29968 Sorted by residual: angle pdb=" CA LEU C 469 " pdb=" CB LEU C 469 " pdb=" CG LEU C 469 " ideal model delta sigma weight residual 116.30 135.77 -19.47 3.50e+00 8.16e-02 3.09e+01 angle pdb=" CA LEU A 469 " pdb=" CB LEU A 469 " pdb=" CG LEU A 469 " ideal model delta sigma weight residual 116.30 135.76 -19.46 3.50e+00 8.16e-02 3.09e+01 angle pdb=" CA LEU B 469 " pdb=" CB LEU B 469 " pdb=" CG LEU B 469 " ideal model delta sigma weight residual 116.30 135.74 -19.44 3.50e+00 8.16e-02 3.08e+01 angle pdb=" CA LEU D 469 " pdb=" CB LEU D 469 " pdb=" CG LEU D 469 " ideal model delta sigma weight residual 116.30 135.69 -19.39 3.50e+00 8.16e-02 3.07e+01 angle pdb=" C THR D 411 " pdb=" N ASN D 412 " pdb=" CA ASN D 412 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.60e+01 ... (remaining 29963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.19: 12905 27.19 - 54.38: 472 54.38 - 81.57: 39 81.57 - 108.76: 12 108.76 - 135.95: 4 Dihedral angle restraints: 13432 sinusoidal: 5680 harmonic: 7752 Sorted by residual: dihedral pdb=" CB CYS C 721 " pdb=" SG CYS C 721 " pdb=" SG CYS C 731 " pdb=" CB CYS C 731 " ideal model delta sinusoidal sigma weight residual -86.00 -156.62 70.62 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CB CYS B 721 " pdb=" SG CYS B 721 " pdb=" SG CYS B 731 " pdb=" CB CYS B 731 " ideal model delta sinusoidal sigma weight residual -86.00 -156.62 70.62 1 1.00e+01 1.00e-02 6.41e+01 dihedral pdb=" CB CYS A 721 " pdb=" SG CYS A 721 " pdb=" SG CYS A 731 " pdb=" CB CYS A 731 " ideal model delta sinusoidal sigma weight residual -86.00 -156.62 70.62 1 1.00e+01 1.00e-02 6.41e+01 ... (remaining 13429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2604 0.054 - 0.108: 656 0.108 - 0.162: 76 0.162 - 0.216: 28 0.216 - 0.270: 12 Chirality restraints: 3376 Sorted by residual: chirality pdb=" CB VAL C 154 " pdb=" CA VAL C 154 " pdb=" CG1 VAL C 154 " pdb=" CG2 VAL C 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CB VAL B 154 " pdb=" CA VAL B 154 " pdb=" CG1 VAL B 154 " pdb=" CG2 VAL B 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" CB VAL D 154 " pdb=" CA VAL D 154 " pdb=" CG1 VAL D 154 " pdb=" CG2 VAL D 154 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 3373 not shown) Planarity restraints: 3708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 180 " -0.040 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO B 181 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO B 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 181 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 180 " 0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO C 181 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 181 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 181 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 180 " -0.040 5.00e-02 4.00e+02 6.11e-02 5.97e+00 pdb=" N PRO A 181 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 181 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 181 " -0.034 5.00e-02 4.00e+02 ... (remaining 3705 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6500 2.82 - 3.34: 19100 3.34 - 3.86: 32240 3.86 - 4.38: 37863 4.38 - 4.90: 64477 Nonbonded interactions: 160180 Sorted by model distance: nonbonded pdb=" OD1 ASP A 322 " pdb=" OH TYR A 359 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASP C 322 " pdb=" OH TYR C 359 " model vdw 2.304 3.040 nonbonded pdb=" OD1 ASP D 322 " pdb=" OH TYR D 359 " model vdw 2.305 3.040 nonbonded pdb=" OD1 ASP B 322 " pdb=" OH TYR B 359 " model vdw 2.305 3.040 nonbonded pdb=" OG SER C 620 " pdb=" NE2 GLN C 646 " model vdw 2.319 3.120 ... (remaining 160175 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 59 through 751 or resid 901 through 902)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 46.270 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.090 22204 Z= 0.419 Angle : 1.169 19.467 29968 Z= 0.608 Chirality : 0.050 0.270 3376 Planarity : 0.006 0.061 3708 Dihedral : 13.070 135.950 8368 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.45 % Favored : 95.40 % Rotamer: Outliers : 0.68 % Allowed : 5.61 % Favored : 93.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.90 (0.10), residues: 2608 helix: -4.63 (0.05), residues: 1440 sheet: -3.55 (0.44), residues: 88 loop : -2.61 (0.15), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 742 HIS 0.006 0.002 HIS A 301 PHE 0.018 0.002 PHE D 316 TYR 0.013 0.002 TYR C 544 ARG 0.009 0.001 ARG B 567 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 621 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8065 (pt0) cc_final: 0.7350 (mm-30) REVERT: A 159 MET cc_start: 0.7002 (tpp) cc_final: 0.6791 (tpp) REVERT: A 193 PHE cc_start: 0.6925 (t80) cc_final: 0.6643 (t80) REVERT: A 201 ASP cc_start: 0.7445 (t70) cc_final: 0.7022 (p0) REVERT: A 318 LYS cc_start: 0.8565 (tttm) cc_final: 0.7907 (ttmt) REVERT: A 358 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7602 (mtpp) REVERT: A 399 THR cc_start: 0.8052 (p) cc_final: 0.7787 (t) REVERT: A 479 MET cc_start: 0.3936 (mmm) cc_final: 0.3678 (mmp) REVERT: A 493 TRP cc_start: 0.7322 (t-100) cc_final: 0.7058 (t-100) REVERT: A 542 PHE cc_start: 0.7288 (m-10) cc_final: 0.5677 (t80) REVERT: A 575 TYR cc_start: 0.7793 (t80) cc_final: 0.7551 (t80) REVERT: A 588 LEU cc_start: 0.9035 (mm) cc_final: 0.8496 (mt) REVERT: A 611 LYS cc_start: 0.6237 (ttpm) cc_final: 0.5726 (mmmm) REVERT: A 627 ASP cc_start: 0.7689 (m-30) cc_final: 0.7445 (m-30) REVERT: A 684 VAL cc_start: 0.7638 (t) cc_final: 0.7274 (t) REVERT: A 688 SER cc_start: 0.7885 (p) cc_final: 0.7279 (m) REVERT: A 743 LYS cc_start: 0.7375 (mtpp) cc_final: 0.6787 (tmtt) REVERT: B 122 ARG cc_start: 0.6909 (mtp85) cc_final: 0.6672 (mtm110) REVERT: B 128 SER cc_start: 0.7025 (m) cc_final: 0.6796 (t) REVERT: B 133 GLU cc_start: 0.7435 (pt0) cc_final: 0.7192 (pt0) REVERT: B 159 MET cc_start: 0.6313 (tpp) cc_final: 0.6042 (tpt) REVERT: B 282 MET cc_start: 0.7213 (mtp) cc_final: 0.6997 (mtp) REVERT: B 358 LYS cc_start: 0.8109 (ttpt) cc_final: 0.7624 (mtpp) REVERT: B 379 ASP cc_start: 0.6184 (p0) cc_final: 0.5917 (t0) REVERT: B 399 THR cc_start: 0.8127 (p) cc_final: 0.7763 (t) REVERT: B 493 TRP cc_start: 0.7374 (t-100) cc_final: 0.7015 (t-100) REVERT: B 542 PHE cc_start: 0.7028 (m-10) cc_final: 0.5550 (t80) REVERT: B 575 TYR cc_start: 0.7808 (t80) cc_final: 0.7600 (t80) REVERT: B 588 LEU cc_start: 0.9051 (mm) cc_final: 0.8514 (mt) REVERT: B 611 LYS cc_start: 0.6295 (ttpm) cc_final: 0.5759 (mmmm) REVERT: B 627 ASP cc_start: 0.7677 (m-30) cc_final: 0.7439 (m-30) REVERT: B 688 SER cc_start: 0.7768 (p) cc_final: 0.7546 (m) REVERT: B 743 LYS cc_start: 0.7581 (mtpp) cc_final: 0.7278 (tmtt) REVERT: C 133 GLU cc_start: 0.7967 (pt0) cc_final: 0.7298 (mm-30) REVERT: C 318 LYS cc_start: 0.8521 (tttm) cc_final: 0.7936 (ttmt) REVERT: C 358 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7901 (ttpp) REVERT: C 399 THR cc_start: 0.8185 (p) cc_final: 0.7912 (t) REVERT: C 435 LYS cc_start: 0.8032 (mtpt) cc_final: 0.7790 (mmmt) REVERT: C 450 PHE cc_start: 0.6834 (t80) cc_final: 0.6505 (t80) REVERT: C 479 MET cc_start: 0.3843 (mmm) cc_final: 0.3442 (mmp) REVERT: C 542 PHE cc_start: 0.7365 (m-10) cc_final: 0.6189 (t80) REVERT: C 555 MET cc_start: 0.8233 (mtm) cc_final: 0.8013 (mtp) REVERT: C 574 MET cc_start: 0.6997 (pp-130) cc_final: 0.6788 (mmt) REVERT: C 588 LEU cc_start: 0.8998 (mm) cc_final: 0.8629 (mt) REVERT: C 611 LYS cc_start: 0.5966 (ttpm) cc_final: 0.5384 (mmmm) REVERT: C 688 SER cc_start: 0.7846 (p) cc_final: 0.6782 (p) REVERT: C 728 PHE cc_start: 0.6832 (m-80) cc_final: 0.6613 (m-80) REVERT: C 743 LYS cc_start: 0.6909 (mtpp) cc_final: 0.6475 (tmtt) REVERT: D 120 LYS cc_start: 0.6720 (mtmp) cc_final: 0.6444 (tttm) REVERT: D 122 ARG cc_start: 0.6899 (mtp85) cc_final: 0.6562 (mtm110) REVERT: D 240 ASP cc_start: 0.7419 (m-30) cc_final: 0.6907 (p0) REVERT: D 356 ILE cc_start: 0.9144 (mm) cc_final: 0.8924 (mt) REVERT: D 358 LYS cc_start: 0.8079 (ttpt) cc_final: 0.7638 (mtpp) REVERT: D 379 ASP cc_start: 0.6168 (p0) cc_final: 0.5629 (t0) REVERT: D 399 THR cc_start: 0.8069 (p) cc_final: 0.7764 (t) REVERT: D 426 HIS cc_start: 0.6704 (t70) cc_final: 0.6452 (t-90) REVERT: D 450 PHE cc_start: 0.7185 (t80) cc_final: 0.6908 (t80) REVERT: D 493 TRP cc_start: 0.7308 (t-100) cc_final: 0.6849 (t-100) REVERT: D 542 PHE cc_start: 0.7145 (m-10) cc_final: 0.5698 (t80) REVERT: D 588 LEU cc_start: 0.9076 (mm) cc_final: 0.8511 (mt) REVERT: D 627 ASP cc_start: 0.7693 (m-30) cc_final: 0.7449 (m-30) REVERT: D 688 SER cc_start: 0.7886 (p) cc_final: 0.7462 (m) REVERT: D 716 ARG cc_start: 0.7233 (tpp-160) cc_final: 0.6938 (tpp80) REVERT: D 743 LYS cc_start: 0.7555 (mtpp) cc_final: 0.6827 (tmtt) outliers start: 16 outliers final: 6 residues processed: 634 average time/residue: 0.3455 time to fit residues: 325.6958 Evaluate side-chains 342 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 336 time to evaluate : 2.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 676 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 676 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 0.2980 chunk 197 optimal weight: 0.1980 chunk 109 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 chunk 132 optimal weight: 0.8980 chunk 105 optimal weight: 7.9990 chunk 203 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 394 ASN ** A 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 683 ASN B 160 HIS B 346 GLN B 394 ASN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN B 683 ASN C 180 ASN C 182 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN C 394 ASN ** C 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 HIS C 646 GLN C 683 ASN C 735 ASN D 178 ASN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN D 394 ASN ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 646 GLN D 683 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22204 Z= 0.151 Angle : 0.631 11.531 29968 Z= 0.317 Chirality : 0.039 0.137 3376 Planarity : 0.004 0.053 3708 Dihedral : 12.069 112.388 3160 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.34 % Allowed : 12.03 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.98 (0.13), residues: 2608 helix: -2.80 (0.09), residues: 1496 sheet: -3.58 (0.46), residues: 88 loop : -1.99 (0.17), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 739 HIS 0.005 0.001 HIS D 160 PHE 0.024 0.001 PHE A 489 TYR 0.016 0.001 TYR D 208 ARG 0.006 0.000 ARG C 690 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 394 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PRO cc_start: 0.6385 (Cg_endo) cc_final: 0.6126 (Cg_exo) REVERT: A 133 GLU cc_start: 0.7751 (pt0) cc_final: 0.7304 (mm-30) REVERT: A 201 ASP cc_start: 0.7479 (t70) cc_final: 0.7166 (p0) REVERT: A 399 THR cc_start: 0.8247 (p) cc_final: 0.7921 (t) REVERT: A 450 PHE cc_start: 0.7035 (t80) cc_final: 0.6529 (t80) REVERT: A 479 MET cc_start: 0.3942 (mmm) cc_final: 0.3642 (mmp) REVERT: A 484 LEU cc_start: 0.4335 (OUTLIER) cc_final: 0.3774 (mt) REVERT: A 493 TRP cc_start: 0.7366 (t-100) cc_final: 0.6884 (t-100) REVERT: A 542 PHE cc_start: 0.7360 (m-10) cc_final: 0.6185 (t80) REVERT: A 561 ASN cc_start: 0.8821 (m110) cc_final: 0.8405 (m110) REVERT: A 588 LEU cc_start: 0.9138 (mm) cc_final: 0.8719 (mt) REVERT: A 611 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5893 (mmmt) REVERT: A 743 LYS cc_start: 0.7281 (mtpp) cc_final: 0.6988 (tmtt) REVERT: B 159 MET cc_start: 0.5804 (tpp) cc_final: 0.5519 (tpt) REVERT: B 282 MET cc_start: 0.7033 (mtp) cc_final: 0.6742 (mtp) REVERT: B 379 ASP cc_start: 0.6414 (p0) cc_final: 0.6069 (t0) REVERT: B 399 THR cc_start: 0.8217 (p) cc_final: 0.7829 (t) REVERT: B 420 LEU cc_start: 0.7658 (mt) cc_final: 0.7441 (mt) REVERT: B 450 PHE cc_start: 0.7097 (t80) cc_final: 0.6404 (t80) REVERT: B 493 TRP cc_start: 0.7365 (t-100) cc_final: 0.6867 (t-100) REVERT: B 542 PHE cc_start: 0.7176 (m-10) cc_final: 0.5566 (t80) REVERT: B 561 ASN cc_start: 0.8794 (m110) cc_final: 0.8371 (m110) REVERT: B 588 LEU cc_start: 0.9073 (mm) cc_final: 0.8697 (mt) REVERT: B 611 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5852 (mmmt) REVERT: C 120 LYS cc_start: 0.7984 (mtmp) cc_final: 0.7699 (mtmt) REVERT: C 133 GLU cc_start: 0.8141 (pt0) cc_final: 0.7382 (mm-30) REVERT: C 399 THR cc_start: 0.8213 (p) cc_final: 0.7878 (t) REVERT: C 450 PHE cc_start: 0.7029 (t80) cc_final: 0.6679 (t80) REVERT: C 479 MET cc_start: 0.4054 (mmm) cc_final: 0.3747 (mmp) REVERT: C 484 LEU cc_start: 0.5504 (OUTLIER) cc_final: 0.5118 (mt) REVERT: C 561 ASN cc_start: 0.8796 (m110) cc_final: 0.8371 (m110) REVERT: C 588 LEU cc_start: 0.9090 (mm) cc_final: 0.8683 (mt) REVERT: C 611 LYS cc_start: 0.6113 (OUTLIER) cc_final: 0.5717 (mmmt) REVERT: C 627 ASP cc_start: 0.7344 (m-30) cc_final: 0.7088 (m-30) REVERT: C 743 LYS cc_start: 0.6959 (mtpp) cc_final: 0.6635 (tmtt) REVERT: D 147 ARG cc_start: 0.5016 (mpt-90) cc_final: 0.4343 (ttp80) REVERT: D 201 ASP cc_start: 0.7352 (t70) cc_final: 0.6874 (p0) REVERT: D 240 ASP cc_start: 0.7515 (m-30) cc_final: 0.6925 (p0) REVERT: D 379 ASP cc_start: 0.6327 (p0) cc_final: 0.5814 (t0) REVERT: D 399 THR cc_start: 0.8227 (p) cc_final: 0.7890 (t) REVERT: D 542 PHE cc_start: 0.7273 (m-10) cc_final: 0.5711 (t80) REVERT: D 561 ASN cc_start: 0.8877 (m110) cc_final: 0.8443 (m110) REVERT: D 588 LEU cc_start: 0.9113 (mm) cc_final: 0.8709 (mt) REVERT: D 611 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5956 (mmmt) REVERT: D 711 LEU cc_start: 0.7688 (tp) cc_final: 0.7390 (tt) REVERT: D 716 ARG cc_start: 0.7318 (tpp-160) cc_final: 0.7076 (tpp-160) REVERT: D 717 MET cc_start: 0.7866 (mtp) cc_final: 0.7652 (mtt) REVERT: D 743 LYS cc_start: 0.7374 (mtpp) cc_final: 0.6974 (tmtt) outliers start: 55 outliers final: 22 residues processed: 435 average time/residue: 0.3113 time to fit residues: 210.9915 Evaluate side-chains 338 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 310 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 481 TRP Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 676 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.9980 chunk 73 optimal weight: 0.0020 chunk 196 optimal weight: 20.0000 chunk 160 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 236 optimal weight: 0.0980 chunk 255 optimal weight: 4.9990 chunk 210 optimal weight: 0.0670 chunk 234 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 189 optimal weight: 4.9990 overall best weight: 0.4326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS B 160 HIS B 216 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 523 HIS D 160 HIS D 216 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22204 Z= 0.118 Angle : 0.554 10.546 29968 Z= 0.270 Chirality : 0.038 0.126 3376 Planarity : 0.003 0.048 3708 Dihedral : 11.234 119.504 3158 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.34 % Allowed : 14.46 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.15), residues: 2608 helix: -1.45 (0.12), residues: 1492 sheet: -2.72 (0.46), residues: 108 loop : -1.51 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 481 HIS 0.004 0.000 HIS A 160 PHE 0.029 0.001 PHE B 590 TYR 0.019 0.001 TYR A 540 ARG 0.004 0.000 ARG A 690 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 375 time to evaluate : 2.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 PRO cc_start: 0.6489 (Cg_endo) cc_final: 0.6276 (Cg_exo) REVERT: A 133 GLU cc_start: 0.7676 (pt0) cc_final: 0.7261 (mm-30) REVERT: A 201 ASP cc_start: 0.7586 (t70) cc_final: 0.7260 (p0) REVERT: A 399 THR cc_start: 0.8209 (p) cc_final: 0.7891 (t) REVERT: A 450 PHE cc_start: 0.6917 (t80) cc_final: 0.6507 (t80) REVERT: A 479 MET cc_start: 0.3798 (mmm) cc_final: 0.3461 (mmp) REVERT: A 484 LEU cc_start: 0.4959 (OUTLIER) cc_final: 0.4361 (mt) REVERT: A 493 TRP cc_start: 0.7315 (t-100) cc_final: 0.6848 (t-100) REVERT: A 542 PHE cc_start: 0.7459 (m-10) cc_final: 0.7186 (m-80) REVERT: A 561 ASN cc_start: 0.8784 (m110) cc_final: 0.8515 (m-40) REVERT: A 588 LEU cc_start: 0.9059 (mm) cc_final: 0.8626 (mt) REVERT: A 611 LYS cc_start: 0.6213 (OUTLIER) cc_final: 0.5816 (mmmt) REVERT: A 743 LYS cc_start: 0.7350 (mtpp) cc_final: 0.7074 (tmtt) REVERT: B 282 MET cc_start: 0.7062 (mtp) cc_final: 0.6753 (mtp) REVERT: B 367 GLU cc_start: 0.6205 (mp0) cc_final: 0.5987 (mp0) REVERT: B 379 ASP cc_start: 0.6299 (p0) cc_final: 0.6039 (t0) REVERT: B 399 THR cc_start: 0.8358 (p) cc_final: 0.8007 (t) REVERT: B 450 PHE cc_start: 0.6912 (t80) cc_final: 0.6440 (t80) REVERT: B 493 TRP cc_start: 0.7416 (t-100) cc_final: 0.6955 (t-100) REVERT: B 542 PHE cc_start: 0.7277 (m-10) cc_final: 0.5685 (t80) REVERT: B 561 ASN cc_start: 0.8782 (m110) cc_final: 0.8347 (m110) REVERT: B 588 LEU cc_start: 0.9005 (mm) cc_final: 0.8616 (mt) REVERT: B 611 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5822 (mmmt) REVERT: C 133 GLU cc_start: 0.8122 (pt0) cc_final: 0.7375 (mm-30) REVERT: C 137 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6829 (mm-30) REVERT: C 399 THR cc_start: 0.8212 (p) cc_final: 0.7896 (t) REVERT: C 450 PHE cc_start: 0.6825 (t80) cc_final: 0.6597 (t80) REVERT: C 484 LEU cc_start: 0.5575 (OUTLIER) cc_final: 0.5286 (mt) REVERT: C 561 ASN cc_start: 0.8727 (m110) cc_final: 0.8439 (m-40) REVERT: C 588 LEU cc_start: 0.9093 (mm) cc_final: 0.8649 (mt) REVERT: C 611 LYS cc_start: 0.6161 (OUTLIER) cc_final: 0.5630 (mmmt) REVERT: C 627 ASP cc_start: 0.7322 (m-30) cc_final: 0.6798 (t0) REVERT: C 743 LYS cc_start: 0.7135 (mtpp) cc_final: 0.6786 (tmtt) REVERT: D 74 GLN cc_start: 0.6521 (mp10) cc_final: 0.6216 (mp10) REVERT: D 147 ARG cc_start: 0.5074 (mpt-90) cc_final: 0.4386 (ttp80) REVERT: D 201 ASP cc_start: 0.7386 (t70) cc_final: 0.6949 (p0) REVERT: D 240 ASP cc_start: 0.7692 (m-30) cc_final: 0.7058 (p0) REVERT: D 254 TYR cc_start: 0.6825 (m-80) cc_final: 0.6579 (m-80) REVERT: D 379 ASP cc_start: 0.6281 (p0) cc_final: 0.5746 (t0) REVERT: D 399 THR cc_start: 0.8187 (p) cc_final: 0.7866 (t) REVERT: D 450 PHE cc_start: 0.7013 (t80) cc_final: 0.6582 (t80) REVERT: D 542 PHE cc_start: 0.7451 (m-10) cc_final: 0.6221 (t80) REVERT: D 561 ASN cc_start: 0.8871 (m110) cc_final: 0.8448 (m110) REVERT: D 588 LEU cc_start: 0.9053 (mm) cc_final: 0.8628 (mt) REVERT: D 611 LYS cc_start: 0.6144 (OUTLIER) cc_final: 0.5818 (mmmt) REVERT: D 716 ARG cc_start: 0.7264 (tpp-160) cc_final: 0.7030 (tpp-160) REVERT: D 743 LYS cc_start: 0.7443 (mtpp) cc_final: 0.7034 (tmtt) outliers start: 55 outliers final: 28 residues processed: 416 average time/residue: 0.3010 time to fit residues: 199.8214 Evaluate side-chains 339 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 305 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 10.0000 chunk 177 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 237 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN C 160 HIS ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22204 Z= 0.362 Angle : 0.760 12.229 29968 Z= 0.378 Chirality : 0.046 0.193 3376 Planarity : 0.005 0.055 3708 Dihedral : 12.404 139.229 3156 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.12 % Allowed : 14.97 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.15), residues: 2608 helix: -1.41 (0.12), residues: 1500 sheet: -2.50 (0.50), residues: 108 loop : -1.69 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 481 HIS 0.006 0.002 HIS C 417 PHE 0.026 0.002 PHE C 590 TYR 0.029 0.002 TYR A 451 ARG 0.007 0.001 ARG D 567 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 307 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7650 (pt0) cc_final: 0.7325 (mm-30) REVERT: A 139 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5796 (tp) REVERT: A 399 THR cc_start: 0.8370 (p) cc_final: 0.8025 (t) REVERT: A 450 PHE cc_start: 0.6914 (t80) cc_final: 0.6451 (t80) REVERT: A 479 MET cc_start: 0.3854 (mmm) cc_final: 0.3522 (mmp) REVERT: A 481 TRP cc_start: 0.3780 (t-100) cc_final: 0.3578 (t60) REVERT: A 493 TRP cc_start: 0.7287 (t-100) cc_final: 0.7042 (t-100) REVERT: A 542 PHE cc_start: 0.7688 (m-10) cc_final: 0.6196 (t80) REVERT: A 561 ASN cc_start: 0.8834 (m110) cc_final: 0.8471 (m110) REVERT: A 588 LEU cc_start: 0.9051 (mm) cc_final: 0.8583 (mt) REVERT: A 611 LYS cc_start: 0.6328 (OUTLIER) cc_final: 0.5833 (mmmt) REVERT: A 627 ASP cc_start: 0.7627 (m-30) cc_final: 0.7317 (t0) REVERT: A 743 LYS cc_start: 0.7356 (mtpp) cc_final: 0.6972 (tmtt) REVERT: B 201 ASP cc_start: 0.7493 (t70) cc_final: 0.7141 (p0) REVERT: B 399 THR cc_start: 0.8452 (p) cc_final: 0.8098 (t) REVERT: B 481 TRP cc_start: 0.2934 (t60) cc_final: 0.2556 (t60) REVERT: B 493 TRP cc_start: 0.7282 (t-100) cc_final: 0.7070 (t-100) REVERT: B 542 PHE cc_start: 0.7456 (m-10) cc_final: 0.5781 (t80) REVERT: B 561 ASN cc_start: 0.8799 (m110) cc_final: 0.8498 (m-40) REVERT: B 574 MET cc_start: 0.6566 (mmm) cc_final: 0.5851 (mmt) REVERT: B 578 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7442 (mpp) REVERT: B 588 LEU cc_start: 0.9049 (mm) cc_final: 0.8541 (mt) REVERT: B 611 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5779 (mmmt) REVERT: B 672 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6844 (ttp) REVERT: C 133 GLU cc_start: 0.8172 (pt0) cc_final: 0.7428 (mm-30) REVERT: C 139 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6179 (tp) REVERT: C 229 ASP cc_start: 0.6524 (m-30) cc_final: 0.6247 (m-30) REVERT: C 399 THR cc_start: 0.8322 (p) cc_final: 0.7965 (t) REVERT: C 484 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5723 (mt) REVERT: C 561 ASN cc_start: 0.8816 (m110) cc_final: 0.8517 (m-40) REVERT: C 574 MET cc_start: 0.7126 (pp-130) cc_final: 0.6874 (mmt) REVERT: C 588 LEU cc_start: 0.9101 (mm) cc_final: 0.8606 (mt) REVERT: C 611 LYS cc_start: 0.6387 (OUTLIER) cc_final: 0.5796 (mmmt) REVERT: C 743 LYS cc_start: 0.7334 (mtpp) cc_final: 0.6894 (tmtt) REVERT: D 201 ASP cc_start: 0.7479 (t70) cc_final: 0.7222 (p0) REVERT: D 399 THR cc_start: 0.8430 (p) cc_final: 0.8047 (t) REVERT: D 450 PHE cc_start: 0.6968 (t80) cc_final: 0.6489 (t80) REVERT: D 484 LEU cc_start: 0.5117 (OUTLIER) cc_final: 0.4398 (mt) REVERT: D 493 TRP cc_start: 0.7363 (t-100) cc_final: 0.6953 (t-100) REVERT: D 542 PHE cc_start: 0.7458 (m-10) cc_final: 0.6113 (t80) REVERT: D 561 ASN cc_start: 0.8859 (m110) cc_final: 0.8497 (m110) REVERT: D 572 MET cc_start: 0.8326 (tpp) cc_final: 0.8078 (tpp) REVERT: D 588 LEU cc_start: 0.9072 (mm) cc_final: 0.8546 (mt) REVERT: D 611 LYS cc_start: 0.6236 (OUTLIER) cc_final: 0.5810 (mmmt) REVERT: D 627 ASP cc_start: 0.7582 (m-30) cc_final: 0.7294 (t0) REVERT: D 716 ARG cc_start: 0.7452 (tpp-160) cc_final: 0.7145 (tpp80) REVERT: D 743 LYS cc_start: 0.7505 (mtpp) cc_final: 0.7057 (tmtt) outliers start: 97 outliers final: 60 residues processed: 385 average time/residue: 0.2973 time to fit residues: 183.3781 Evaluate side-chains 338 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 268 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 620 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 68 MET Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 484 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 596 LEU Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 620 SER Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 9.9990 chunk 142 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 chunk 173 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 292 GLN ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22204 Z= 0.262 Angle : 0.662 14.205 29968 Z= 0.326 Chirality : 0.042 0.155 3376 Planarity : 0.004 0.070 3708 Dihedral : 11.637 130.790 3156 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.55 % Allowed : 15.56 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.15), residues: 2608 helix: -1.06 (0.12), residues: 1496 sheet: -2.70 (0.49), residues: 108 loop : -1.65 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP C 481 HIS 0.004 0.001 HIS A 417 PHE 0.023 0.002 PHE C 590 TYR 0.023 0.002 TYR A 451 ARG 0.005 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 293 time to evaluate : 2.421 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7774 (pt0) cc_final: 0.7333 (mm-30) REVERT: A 139 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.5824 (tp) REVERT: A 399 THR cc_start: 0.8322 (p) cc_final: 0.7975 (t) REVERT: A 450 PHE cc_start: 0.6844 (t80) cc_final: 0.6347 (t80) REVERT: A 479 MET cc_start: 0.3815 (mmm) cc_final: 0.3424 (mmp) REVERT: A 481 TRP cc_start: 0.3783 (t-100) cc_final: 0.3489 (t60) REVERT: A 493 TRP cc_start: 0.7354 (t-100) cc_final: 0.6980 (t-100) REVERT: A 542 PHE cc_start: 0.7654 (m-10) cc_final: 0.6266 (t80) REVERT: A 561 ASN cc_start: 0.8760 (m110) cc_final: 0.8365 (m110) REVERT: A 588 LEU cc_start: 0.9062 (mm) cc_final: 0.8609 (mt) REVERT: A 611 LYS cc_start: 0.6085 (OUTLIER) cc_final: 0.5643 (mmmt) REVERT: A 743 LYS cc_start: 0.7294 (mtpp) cc_final: 0.6892 (tmtt) REVERT: B 62 PRO cc_start: 0.6549 (Cg_endo) cc_final: 0.6340 (Cg_exo) REVERT: B 162 LEU cc_start: 0.6094 (OUTLIER) cc_final: 0.5584 (mm) REVERT: B 163 THR cc_start: 0.7813 (p) cc_final: 0.7599 (t) REVERT: B 201 ASP cc_start: 0.7357 (t70) cc_final: 0.7146 (p0) REVERT: B 320 MET cc_start: 0.8200 (mmm) cc_final: 0.7884 (mmt) REVERT: B 399 THR cc_start: 0.8358 (p) cc_final: 0.8034 (t) REVERT: B 450 PHE cc_start: 0.6857 (t80) cc_final: 0.6362 (t80) REVERT: B 481 TRP cc_start: 0.2741 (t60) cc_final: 0.2408 (t60) REVERT: B 493 TRP cc_start: 0.7327 (t-100) cc_final: 0.6961 (t-100) REVERT: B 542 PHE cc_start: 0.7532 (m-10) cc_final: 0.5864 (t80) REVERT: B 561 ASN cc_start: 0.8720 (m110) cc_final: 0.8354 (m110) REVERT: B 574 MET cc_start: 0.6494 (mmm) cc_final: 0.5770 (mmt) REVERT: B 578 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7134 (mpp) REVERT: B 588 LEU cc_start: 0.9033 (mm) cc_final: 0.8589 (mt) REVERT: B 611 LYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5678 (mmmt) REVERT: C 133 GLU cc_start: 0.8099 (pt0) cc_final: 0.7448 (mm-30) REVERT: C 139 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6165 (tp) REVERT: C 148 ARG cc_start: 0.5586 (mpt90) cc_final: 0.4937 (mmp80) REVERT: C 229 ASP cc_start: 0.6431 (m-30) cc_final: 0.6159 (m-30) REVERT: C 399 THR cc_start: 0.8333 (p) cc_final: 0.7981 (t) REVERT: C 484 LEU cc_start: 0.5855 (OUTLIER) cc_final: 0.5629 (mt) REVERT: C 535 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8150 (tp) REVERT: C 561 ASN cc_start: 0.8678 (m110) cc_final: 0.8297 (m110) REVERT: C 574 MET cc_start: 0.7207 (pp-130) cc_final: 0.6938 (mmt) REVERT: C 588 LEU cc_start: 0.9084 (mm) cc_final: 0.8596 (mt) REVERT: C 611 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.5740 (mmmt) REVERT: C 743 LYS cc_start: 0.7270 (mtpp) cc_final: 0.6794 (tmtt) REVERT: D 139 LEU cc_start: 0.5585 (OUTLIER) cc_final: 0.5228 (tp) REVERT: D 180 ASN cc_start: 0.6623 (m-40) cc_final: 0.6295 (p0) REVERT: D 193 PHE cc_start: 0.7019 (t80) cc_final: 0.6568 (t80) REVERT: D 320 MET cc_start: 0.8565 (mmm) cc_final: 0.8270 (mpp) REVERT: D 361 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7448 (mm) REVERT: D 399 THR cc_start: 0.8383 (p) cc_final: 0.8020 (t) REVERT: D 450 PHE cc_start: 0.6952 (t80) cc_final: 0.6567 (t80) REVERT: D 481 TRP cc_start: 0.3040 (t60) cc_final: 0.2756 (t60) REVERT: D 542 PHE cc_start: 0.7517 (m-10) cc_final: 0.6290 (t80) REVERT: D 561 ASN cc_start: 0.8810 (m110) cc_final: 0.8398 (m110) REVERT: D 572 MET cc_start: 0.8277 (tpp) cc_final: 0.8037 (tpp) REVERT: D 588 LEU cc_start: 0.9070 (mm) cc_final: 0.8597 (mt) REVERT: D 611 LYS cc_start: 0.6105 (OUTLIER) cc_final: 0.5660 (mmmt) REVERT: D 743 LYS cc_start: 0.7398 (mtpp) cc_final: 0.7026 (tmtt) outliers start: 107 outliers final: 61 residues processed: 377 average time/residue: 0.3237 time to fit residues: 196.6516 Evaluate side-chains 351 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 278 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASN Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 366 LYS Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 1.9990 chunk 226 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 147 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 251 optimal weight: 3.9990 chunk 208 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22204 Z= 0.174 Angle : 0.583 12.728 29968 Z= 0.287 Chirality : 0.040 0.141 3376 Planarity : 0.004 0.071 3708 Dihedral : 10.915 124.394 3154 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 4.08 % Allowed : 16.50 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.16), residues: 2608 helix: -0.56 (0.13), residues: 1476 sheet: -2.93 (0.48), residues: 108 loop : -1.59 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 481 HIS 0.003 0.001 HIS B 523 PHE 0.021 0.001 PHE C 590 TYR 0.022 0.001 TYR B 451 ARG 0.005 0.000 ARG D 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 291 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7784 (pt0) cc_final: 0.7314 (mm-30) REVERT: A 139 LEU cc_start: 0.6395 (OUTLIER) cc_final: 0.5815 (tp) REVERT: A 180 ASN cc_start: 0.6510 (OUTLIER) cc_final: 0.6267 (p0) REVERT: A 399 THR cc_start: 0.8311 (p) cc_final: 0.7984 (t) REVERT: A 443 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8434 (mp) REVERT: A 450 PHE cc_start: 0.6838 (t80) cc_final: 0.6346 (t80) REVERT: A 479 MET cc_start: 0.3821 (mmm) cc_final: 0.3460 (mmp) REVERT: A 481 TRP cc_start: 0.3806 (t-100) cc_final: 0.3556 (t60) REVERT: A 493 TRP cc_start: 0.7362 (t-100) cc_final: 0.7011 (t-100) REVERT: A 542 PHE cc_start: 0.7704 (m-10) cc_final: 0.6307 (t80) REVERT: A 561 ASN cc_start: 0.8707 (m110) cc_final: 0.8345 (m110) REVERT: A 588 LEU cc_start: 0.9063 (mm) cc_final: 0.8682 (mt) REVERT: A 611 LYS cc_start: 0.6273 (OUTLIER) cc_final: 0.5740 (mmmt) REVERT: A 702 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7884 (tp30) REVERT: A 743 LYS cc_start: 0.7284 (mtpp) cc_final: 0.6834 (tmtt) REVERT: B 62 PRO cc_start: 0.6516 (Cg_endo) cc_final: 0.6305 (Cg_exo) REVERT: B 162 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5751 (mm) REVERT: B 399 THR cc_start: 0.8412 (p) cc_final: 0.8073 (t) REVERT: B 443 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8449 (mp) REVERT: B 450 PHE cc_start: 0.6888 (t80) cc_final: 0.6397 (t80) REVERT: B 481 TRP cc_start: 0.2765 (t60) cc_final: 0.2505 (t60) REVERT: B 493 TRP cc_start: 0.7293 (t-100) cc_final: 0.6935 (t-100) REVERT: B 542 PHE cc_start: 0.7632 (m-10) cc_final: 0.6241 (t80) REVERT: B 561 ASN cc_start: 0.8698 (m110) cc_final: 0.8338 (m110) REVERT: B 574 MET cc_start: 0.6443 (mmm) cc_final: 0.5782 (mmt) REVERT: B 578 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7185 (mpp) REVERT: B 588 LEU cc_start: 0.9044 (mm) cc_final: 0.8572 (mt) REVERT: B 611 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5672 (mmmt) REVERT: C 133 GLU cc_start: 0.8028 (pt0) cc_final: 0.7388 (mm-30) REVERT: C 139 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6306 (tt) REVERT: C 148 ARG cc_start: 0.5465 (mpt90) cc_final: 0.4936 (mmp80) REVERT: C 162 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6644 (mm) REVERT: C 169 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7601 (ttmt) REVERT: C 399 THR cc_start: 0.8327 (p) cc_final: 0.7981 (t) REVERT: C 443 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8403 (mp) REVERT: C 484 LEU cc_start: 0.5483 (OUTLIER) cc_final: 0.5279 (mt) REVERT: C 535 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8166 (tp) REVERT: C 561 ASN cc_start: 0.8643 (m110) cc_final: 0.8324 (m110) REVERT: C 588 LEU cc_start: 0.9089 (mm) cc_final: 0.8663 (mt) REVERT: C 611 LYS cc_start: 0.6331 (OUTLIER) cc_final: 0.5823 (mmmt) REVERT: C 627 ASP cc_start: 0.7271 (m-30) cc_final: 0.7070 (m-30) REVERT: C 743 LYS cc_start: 0.7210 (mtpp) cc_final: 0.6791 (tmtt) REVERT: D 120 LYS cc_start: 0.6040 (tttm) cc_final: 0.5535 (mtmt) REVERT: D 139 LEU cc_start: 0.5737 (OUTLIER) cc_final: 0.5260 (tp) REVERT: D 320 MET cc_start: 0.8531 (mmm) cc_final: 0.8194 (mpp) REVERT: D 361 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7461 (mm) REVERT: D 399 THR cc_start: 0.8380 (p) cc_final: 0.8023 (t) REVERT: D 450 PHE cc_start: 0.6882 (t80) cc_final: 0.6469 (t80) REVERT: D 481 TRP cc_start: 0.2910 (t60) cc_final: 0.2652 (t60) REVERT: D 542 PHE cc_start: 0.7501 (m-10) cc_final: 0.6248 (t80) REVERT: D 561 ASN cc_start: 0.8725 (m110) cc_final: 0.8361 (m110) REVERT: D 572 MET cc_start: 0.8185 (tpp) cc_final: 0.7975 (tpp) REVERT: D 588 LEU cc_start: 0.9082 (mm) cc_final: 0.8649 (mt) REVERT: D 611 LYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5648 (mmmt) REVERT: D 743 LYS cc_start: 0.7319 (mtpp) cc_final: 0.7004 (tmtt) outliers start: 96 outliers final: 47 residues processed: 369 average time/residue: 0.2929 time to fit residues: 173.4285 Evaluate side-chains 341 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 275 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 538 PHE Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 143 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 250 optimal weight: 0.9980 chunk 156 optimal weight: 2.9990 chunk 152 optimal weight: 4.9990 chunk 115 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22204 Z= 0.188 Angle : 0.594 12.315 29968 Z= 0.292 Chirality : 0.040 0.142 3376 Planarity : 0.004 0.068 3708 Dihedral : 10.786 124.631 3154 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.12 % Allowed : 16.79 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.16), residues: 2608 helix: -0.40 (0.13), residues: 1480 sheet: -3.06 (0.46), residues: 108 loop : -1.54 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 481 HIS 0.003 0.001 HIS B 523 PHE 0.021 0.001 PHE C 590 TYR 0.021 0.001 TYR B 451 ARG 0.005 0.000 ARG D 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 291 time to evaluate : 2.745 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7750 (pt0) cc_final: 0.7279 (mm-30) REVERT: A 139 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5915 (tp) REVERT: A 229 ASP cc_start: 0.6568 (m-30) cc_final: 0.5943 (t0) REVERT: A 399 THR cc_start: 0.8317 (p) cc_final: 0.7973 (t) REVERT: A 443 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 450 PHE cc_start: 0.6824 (t80) cc_final: 0.6352 (t80) REVERT: A 479 MET cc_start: 0.3854 (mmm) cc_final: 0.3485 (mmp) REVERT: A 493 TRP cc_start: 0.7383 (t-100) cc_final: 0.7046 (t-100) REVERT: A 542 PHE cc_start: 0.7696 (m-10) cc_final: 0.6306 (t80) REVERT: A 561 ASN cc_start: 0.8803 (m110) cc_final: 0.8378 (m110) REVERT: A 611 LYS cc_start: 0.6249 (OUTLIER) cc_final: 0.5609 (mmmm) REVERT: A 743 LYS cc_start: 0.7259 (mtpp) cc_final: 0.6832 (tmtt) REVERT: B 361 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7412 (mm) REVERT: B 399 THR cc_start: 0.8411 (p) cc_final: 0.8086 (t) REVERT: B 443 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8428 (mp) REVERT: B 450 PHE cc_start: 0.6880 (t80) cc_final: 0.6391 (t80) REVERT: B 493 TRP cc_start: 0.7282 (t-100) cc_final: 0.6934 (t-100) REVERT: B 542 PHE cc_start: 0.7641 (m-10) cc_final: 0.6282 (t80) REVERT: B 561 ASN cc_start: 0.8751 (m110) cc_final: 0.8328 (m110) REVERT: B 574 MET cc_start: 0.6460 (mmm) cc_final: 0.5789 (mmt) REVERT: B 578 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7176 (mpp) REVERT: B 588 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8548 (mt) REVERT: B 611 LYS cc_start: 0.6190 (OUTLIER) cc_final: 0.5543 (mmmm) REVERT: C 133 GLU cc_start: 0.8046 (pt0) cc_final: 0.7402 (mm-30) REVERT: C 139 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6414 (tt) REVERT: C 148 ARG cc_start: 0.5379 (mpt90) cc_final: 0.4909 (mmp80) REVERT: C 162 LEU cc_start: 0.6670 (OUTLIER) cc_final: 0.6409 (mm) REVERT: C 169 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7683 (ttmm) REVERT: C 399 THR cc_start: 0.8276 (p) cc_final: 0.7945 (t) REVERT: C 484 LEU cc_start: 0.5375 (OUTLIER) cc_final: 0.4885 (mt) REVERT: C 535 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8162 (tp) REVERT: C 561 ASN cc_start: 0.8646 (m110) cc_final: 0.8266 (m110) REVERT: C 588 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8661 (mt) REVERT: C 611 LYS cc_start: 0.6326 (OUTLIER) cc_final: 0.5774 (mmmt) REVERT: C 743 LYS cc_start: 0.7204 (mtpp) cc_final: 0.6777 (tmtt) REVERT: D 120 LYS cc_start: 0.6113 (tttm) cc_final: 0.5699 (mtmt) REVERT: D 139 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5473 (tp) REVERT: D 320 MET cc_start: 0.8547 (mmm) cc_final: 0.8179 (mpp) REVERT: D 361 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7456 (mm) REVERT: D 399 THR cc_start: 0.8354 (p) cc_final: 0.8015 (t) REVERT: D 450 PHE cc_start: 0.6872 (t80) cc_final: 0.6480 (t80) REVERT: D 481 TRP cc_start: 0.3003 (t60) cc_final: 0.2748 (t60) REVERT: D 542 PHE cc_start: 0.7546 (m-10) cc_final: 0.6301 (t80) REVERT: D 561 ASN cc_start: 0.8796 (m110) cc_final: 0.8375 (m110) REVERT: D 588 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8556 (mt) REVERT: D 611 LYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5526 (mmmm) REVERT: D 743 LYS cc_start: 0.7353 (mtpp) cc_final: 0.6998 (tmtt) outliers start: 97 outliers final: 59 residues processed: 368 average time/residue: 0.2909 time to fit residues: 172.4034 Evaluate side-chains 351 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 273 time to evaluate : 2.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 144 ASP Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 149 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 170 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 196 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22204 Z= 0.208 Angle : 0.600 12.085 29968 Z= 0.296 Chirality : 0.040 0.143 3376 Planarity : 0.004 0.076 3708 Dihedral : 10.854 125.397 3154 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 4.04 % Allowed : 17.26 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.16), residues: 2608 helix: -0.36 (0.13), residues: 1500 sheet: -3.07 (0.45), residues: 108 loop : -1.58 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 481 HIS 0.003 0.001 HIS A 417 PHE 0.029 0.001 PHE D 193 TYR 0.021 0.001 TYR B 451 ARG 0.004 0.000 ARG A 567 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 280 time to evaluate : 2.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 GLU cc_start: 0.7815 (pt0) cc_final: 0.7362 (mm-30) REVERT: A 139 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6054 (tt) REVERT: A 229 ASP cc_start: 0.6561 (m-30) cc_final: 0.6111 (t0) REVERT: A 399 THR cc_start: 0.8334 (p) cc_final: 0.7984 (t) REVERT: A 443 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 450 PHE cc_start: 0.6850 (t80) cc_final: 0.6365 (t80) REVERT: A 479 MET cc_start: 0.4061 (mmm) cc_final: 0.3733 (mmp) REVERT: A 493 TRP cc_start: 0.7348 (t-100) cc_final: 0.7016 (t-100) REVERT: A 542 PHE cc_start: 0.7681 (m-10) cc_final: 0.6262 (t80) REVERT: A 561 ASN cc_start: 0.8713 (m110) cc_final: 0.8363 (m110) REVERT: A 588 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8631 (mt) REVERT: A 611 LYS cc_start: 0.6288 (OUTLIER) cc_final: 0.5615 (mmmm) REVERT: A 743 LYS cc_start: 0.7171 (mtpp) cc_final: 0.6787 (tmtt) REVERT: B 120 LYS cc_start: 0.6155 (tttm) cc_final: 0.5801 (mtmt) REVERT: B 124 PHE cc_start: 0.7393 (OUTLIER) cc_final: 0.7070 (t80) REVERT: B 159 MET cc_start: 0.6710 (tpt) cc_final: 0.6457 (tpt) REVERT: B 361 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7436 (mm) REVERT: B 399 THR cc_start: 0.8449 (p) cc_final: 0.8127 (t) REVERT: B 450 PHE cc_start: 0.6846 (t80) cc_final: 0.6344 (t80) REVERT: B 493 TRP cc_start: 0.7276 (t-100) cc_final: 0.6951 (t-100) REVERT: B 542 PHE cc_start: 0.7633 (m-10) cc_final: 0.6260 (t80) REVERT: B 561 ASN cc_start: 0.8743 (m110) cc_final: 0.8388 (m110) REVERT: B 574 MET cc_start: 0.6548 (mmm) cc_final: 0.5841 (mmt) REVERT: B 578 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7226 (mpp) REVERT: B 588 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8532 (mt) REVERT: B 611 LYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5490 (mmmm) REVERT: C 133 GLU cc_start: 0.8005 (pt0) cc_final: 0.7372 (mm-30) REVERT: C 139 LEU cc_start: 0.6870 (OUTLIER) cc_final: 0.6497 (tt) REVERT: C 148 ARG cc_start: 0.5330 (mpt90) cc_final: 0.4900 (mmp80) REVERT: C 158 LEU cc_start: 0.7294 (tp) cc_final: 0.6892 (pp) REVERT: C 162 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6472 (mm) REVERT: C 169 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7670 (ttmm) REVERT: C 399 THR cc_start: 0.8306 (p) cc_final: 0.7965 (t) REVERT: C 484 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.4950 (mt) REVERT: C 535 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8154 (tp) REVERT: C 561 ASN cc_start: 0.8601 (m110) cc_final: 0.8256 (m110) REVERT: C 588 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8614 (mt) REVERT: C 611 LYS cc_start: 0.6355 (OUTLIER) cc_final: 0.5778 (mmmt) REVERT: C 743 LYS cc_start: 0.7235 (mtpp) cc_final: 0.6786 (tmtt) REVERT: D 120 LYS cc_start: 0.6217 (tttm) cc_final: 0.5746 (mtmt) REVERT: D 139 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5643 (tp) REVERT: D 320 MET cc_start: 0.8500 (mmm) cc_final: 0.8161 (mpp) REVERT: D 361 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7512 (mm) REVERT: D 399 THR cc_start: 0.8380 (p) cc_final: 0.8028 (t) REVERT: D 450 PHE cc_start: 0.6921 (t80) cc_final: 0.6538 (t80) REVERT: D 542 PHE cc_start: 0.7568 (m-10) cc_final: 0.6310 (t80) REVERT: D 561 ASN cc_start: 0.8731 (m110) cc_final: 0.8373 (m110) REVERT: D 588 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8603 (mt) REVERT: D 611 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5510 (mmmm) REVERT: D 743 LYS cc_start: 0.7355 (mtpp) cc_final: 0.6989 (tmtt) outliers start: 95 outliers final: 66 residues processed: 354 average time/residue: 0.3015 time to fit residues: 170.4517 Evaluate side-chains 349 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 263 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 607 SER Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 219 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 211 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22204 Z= 0.176 Angle : 0.575 11.782 29968 Z= 0.284 Chirality : 0.039 0.147 3376 Planarity : 0.004 0.074 3708 Dihedral : 10.600 122.595 3154 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.91 % Allowed : 17.77 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.16), residues: 2608 helix: -0.19 (0.13), residues: 1484 sheet: -3.09 (0.45), residues: 108 loop : -1.52 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 481 HIS 0.003 0.001 HIS B 523 PHE 0.019 0.001 PHE C 590 TYR 0.020 0.001 TYR B 451 ARG 0.003 0.000 ARG D 487 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 279 time to evaluate : 2.599 Fit side-chains REVERT: A 133 GLU cc_start: 0.7839 (pt0) cc_final: 0.7327 (mm-30) REVERT: A 139 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6099 (tt) REVERT: A 229 ASP cc_start: 0.6561 (m-30) cc_final: 0.5941 (m-30) REVERT: A 399 THR cc_start: 0.8313 (p) cc_final: 0.7972 (t) REVERT: A 450 PHE cc_start: 0.6830 (t80) cc_final: 0.6337 (t80) REVERT: A 479 MET cc_start: 0.3940 (mmm) cc_final: 0.3578 (mmp) REVERT: A 493 TRP cc_start: 0.7356 (t-100) cc_final: 0.7012 (t-100) REVERT: A 542 PHE cc_start: 0.7699 (m-10) cc_final: 0.6283 (t80) REVERT: A 561 ASN cc_start: 0.8703 (m110) cc_final: 0.8327 (m110) REVERT: A 611 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5522 (mmmm) REVERT: A 702 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7880 (tp30) REVERT: A 743 LYS cc_start: 0.7171 (mtpp) cc_final: 0.6777 (tmtt) REVERT: B 120 LYS cc_start: 0.6026 (tttm) cc_final: 0.5738 (mtmt) REVERT: B 124 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.7078 (t80) REVERT: B 159 MET cc_start: 0.6770 (tpt) cc_final: 0.6525 (tpt) REVERT: B 201 ASP cc_start: 0.7425 (t70) cc_final: 0.7185 (p0) REVERT: B 361 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7461 (mm) REVERT: B 399 THR cc_start: 0.8466 (p) cc_final: 0.8152 (t) REVERT: B 450 PHE cc_start: 0.6825 (t80) cc_final: 0.6333 (t80) REVERT: B 493 TRP cc_start: 0.7291 (t-100) cc_final: 0.6967 (t-100) REVERT: B 561 ASN cc_start: 0.8690 (m110) cc_final: 0.8309 (m110) REVERT: B 574 MET cc_start: 0.6495 (mmm) cc_final: 0.5842 (mmt) REVERT: B 578 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7229 (mpp) REVERT: B 588 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8558 (mt) REVERT: B 611 LYS cc_start: 0.6185 (OUTLIER) cc_final: 0.5543 (mmmm) REVERT: C 133 GLU cc_start: 0.7989 (pt0) cc_final: 0.7355 (mm-30) REVERT: C 139 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6516 (tt) REVERT: C 148 ARG cc_start: 0.5268 (mpt90) cc_final: 0.4838 (mmp80) REVERT: C 158 LEU cc_start: 0.7283 (tp) cc_final: 0.6894 (pp) REVERT: C 162 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6333 (mm) REVERT: C 169 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7541 (ttmt) REVERT: C 399 THR cc_start: 0.8301 (p) cc_final: 0.7982 (t) REVERT: C 450 PHE cc_start: 0.6793 (t80) cc_final: 0.6413 (t80) REVERT: C 484 LEU cc_start: 0.5153 (OUTLIER) cc_final: 0.4802 (mt) REVERT: C 535 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8208 (tp) REVERT: C 561 ASN cc_start: 0.8603 (m110) cc_final: 0.8263 (m110) REVERT: C 588 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8603 (mt) REVERT: C 611 LYS cc_start: 0.6323 (OUTLIER) cc_final: 0.5783 (mmmt) REVERT: C 627 ASP cc_start: 0.7201 (m-30) cc_final: 0.6961 (m-30) REVERT: C 743 LYS cc_start: 0.7123 (mtpp) cc_final: 0.6709 (tmtt) REVERT: D 120 LYS cc_start: 0.6174 (tttm) cc_final: 0.5770 (mtmt) REVERT: D 139 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.5823 (tp) REVERT: D 320 MET cc_start: 0.8480 (mmm) cc_final: 0.8114 (mpp) REVERT: D 361 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7552 (mm) REVERT: D 399 THR cc_start: 0.8384 (p) cc_final: 0.8037 (t) REVERT: D 450 PHE cc_start: 0.6909 (t80) cc_final: 0.6548 (t80) REVERT: D 542 PHE cc_start: 0.7566 (m-10) cc_final: 0.6258 (t80) REVERT: D 561 ASN cc_start: 0.8723 (m110) cc_final: 0.8324 (m110) REVERT: D 588 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8589 (mt) REVERT: D 611 LYS cc_start: 0.6129 (OUTLIER) cc_final: 0.5499 (mmmm) REVERT: D 702 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7843 (tp30) REVERT: D 743 LYS cc_start: 0.7322 (mtpp) cc_final: 0.6950 (tmtt) outliers start: 92 outliers final: 62 residues processed: 348 average time/residue: 0.2940 time to fit residues: 163.9351 Evaluate side-chains 347 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 265 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 702 GLU Chi-restraints excluded: chain A residue 704 GLU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 361 LEU Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 407 ILE Chi-restraints excluded: chain B residue 458 VAL Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 611 LYS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 71 ASN Chi-restraints excluded: chain C residue 139 LEU Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 169 LYS Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 396 ASP Chi-restraints excluded: chain C residue 407 ILE Chi-restraints excluded: chain C residue 458 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 535 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 611 LYS Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 186 ILE Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 611 LYS Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 672 MET Chi-restraints excluded: chain D residue 673 LEU Chi-restraints excluded: chain D residue 702 GLU Chi-restraints excluded: chain D residue 704 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 7.9990 chunk 246 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 117 optimal weight: 0.0370 chunk 171 optimal weight: 0.0970 chunk 259 optimal weight: 0.8980 chunk 238 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 159 optimal weight: 0.5980 chunk 126 optimal weight: 0.6980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22204 Z= 0.125 Angle : 0.535 11.615 29968 Z= 0.261 Chirality : 0.038 0.161 3376 Planarity : 0.004 0.063 3708 Dihedral : 9.612 106.533 3154 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.13 % Allowed : 19.69 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.16), residues: 2608 helix: 0.15 (0.13), residues: 1496 sheet: -3.11 (0.45), residues: 108 loop : -1.45 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 481 HIS 0.002 0.000 HIS B 523 PHE 0.022 0.001 PHE D 590 TYR 0.018 0.001 TYR B 451 ARG 0.004 0.000 ARG D 487 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5216 Ramachandran restraints generated. 2608 Oldfield, 0 Emsley, 2608 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 310 time to evaluate : 2.507 Fit side-chains REVERT: A 133 GLU cc_start: 0.7736 (pt0) cc_final: 0.7225 (mm-30) REVERT: A 399 THR cc_start: 0.8358 (p) cc_final: 0.8066 (t) REVERT: A 450 PHE cc_start: 0.6827 (t80) cc_final: 0.6353 (t80) REVERT: A 479 MET cc_start: 0.4022 (mmm) cc_final: 0.3673 (mmp) REVERT: A 493 TRP cc_start: 0.7356 (t-100) cc_final: 0.6939 (t-100) REVERT: A 542 PHE cc_start: 0.7729 (m-10) cc_final: 0.6317 (t80) REVERT: A 561 ASN cc_start: 0.8698 (m110) cc_final: 0.8289 (m110) REVERT: A 588 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8766 (mm) REVERT: A 611 LYS cc_start: 0.6076 (ttpm) cc_final: 0.5441 (mmmm) REVERT: A 743 LYS cc_start: 0.7114 (mtpp) cc_final: 0.6762 (tmtt) REVERT: B 74 GLN cc_start: 0.6135 (mm-40) cc_final: 0.5583 (tp40) REVERT: B 124 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.7067 (t80) REVERT: B 159 MET cc_start: 0.6717 (tpt) cc_final: 0.6415 (tpt) REVERT: B 365 ILE cc_start: 0.6481 (mm) cc_final: 0.6118 (pt) REVERT: B 367 GLU cc_start: 0.6648 (mp0) cc_final: 0.6222 (mp0) REVERT: B 399 THR cc_start: 0.8407 (p) cc_final: 0.8112 (t) REVERT: B 450 PHE cc_start: 0.6840 (t80) cc_final: 0.6366 (t80) REVERT: B 493 TRP cc_start: 0.7321 (t-100) cc_final: 0.6937 (t-100) REVERT: B 561 ASN cc_start: 0.8670 (m110) cc_final: 0.8267 (m110) REVERT: B 574 MET cc_start: 0.6309 (mmm) cc_final: 0.5440 (mmp) REVERT: B 578 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7288 (mpp) REVERT: B 588 LEU cc_start: 0.8964 (mm) cc_final: 0.8565 (mt) REVERT: B 590 PHE cc_start: 0.9148 (t80) cc_final: 0.8908 (t80) REVERT: B 611 LYS cc_start: 0.5944 (ttpm) cc_final: 0.5331 (mmmm) REVERT: C 133 GLU cc_start: 0.7904 (pt0) cc_final: 0.7261 (mm-30) REVERT: C 148 ARG cc_start: 0.5261 (mpt90) cc_final: 0.4848 (mmp80) REVERT: C 158 LEU cc_start: 0.7307 (tp) cc_final: 0.6961 (pp) REVERT: C 162 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6418 (mm) REVERT: C 399 THR cc_start: 0.8312 (p) cc_final: 0.8042 (t) REVERT: C 450 PHE cc_start: 0.6699 (t80) cc_final: 0.6306 (t80) REVERT: C 484 LEU cc_start: 0.5034 (OUTLIER) cc_final: 0.4776 (mt) REVERT: C 561 ASN cc_start: 0.8607 (m110) cc_final: 0.8239 (m110) REVERT: C 611 LYS cc_start: 0.6234 (ttpm) cc_final: 0.5601 (mmmm) REVERT: C 627 ASP cc_start: 0.7186 (m-30) cc_final: 0.6882 (m-30) REVERT: C 743 LYS cc_start: 0.7067 (mtpp) cc_final: 0.6701 (tmtt) REVERT: D 74 GLN cc_start: 0.6675 (mp10) cc_final: 0.6199 (mp10) REVERT: D 120 LYS cc_start: 0.5986 (tttm) cc_final: 0.5731 (mtmt) REVERT: D 139 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.5782 (tp) REVERT: D 159 MET cc_start: 0.6694 (tpp) cc_final: 0.6454 (tpt) REVERT: D 320 MET cc_start: 0.8495 (mmm) cc_final: 0.8107 (mpp) REVERT: D 399 THR cc_start: 0.8402 (p) cc_final: 0.8091 (t) REVERT: D 450 PHE cc_start: 0.6845 (t80) cc_final: 0.6462 (t80) REVERT: D 479 MET cc_start: 0.4281 (mmt) cc_final: 0.4042 (mmp) REVERT: D 501 GLU cc_start: 0.7285 (mp0) cc_final: 0.7043 (mp0) REVERT: D 561 ASN cc_start: 0.8710 (m110) cc_final: 0.8292 (m110) REVERT: D 574 MET cc_start: 0.6701 (mmt) cc_final: 0.5954 (ppp) REVERT: D 581 LYS cc_start: 0.8149 (mmmm) cc_final: 0.7902 (mmtt) REVERT: D 588 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8542 (mt) REVERT: D 611 LYS cc_start: 0.5979 (ttpm) cc_final: 0.5366 (mmmm) REVERT: D 743 LYS cc_start: 0.7269 (mtpp) cc_final: 0.6891 (tmtt) outliers start: 50 outliers final: 34 residues processed: 351 average time/residue: 0.3016 time to fit residues: 167.8919 Evaluate side-chains 318 residues out of total 2352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 277 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 458 VAL Chi-restraints excluded: chain A residue 484 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 710 TRP Chi-restraints excluded: chain A residue 736 GLU Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 484 LEU Chi-restraints excluded: chain B residue 578 MET Chi-restraints excluded: chain B residue 607 SER Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 704 GLU Chi-restraints excluded: chain B residue 710 TRP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 591 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 704 GLU Chi-restraints excluded: chain C residue 710 TRP Chi-restraints excluded: chain C residue 740 THR Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 458 VAL Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 591 LEU Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 7.9990 chunk 219 optimal weight: 1.9990 chunk 63 optimal weight: 7.9990 chunk 190 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 206 optimal weight: 0.0020 chunk 86 optimal weight: 0.0980 chunk 212 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS B 216 GLN ** B 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.135323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104348 restraints weight = 41652.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.107328 restraints weight = 26589.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.109301 restraints weight = 20184.859| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3379 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22204 Z= 0.128 Angle : 0.533 11.479 29968 Z= 0.260 Chirality : 0.038 0.156 3376 Planarity : 0.004 0.058 3708 Dihedral : 9.287 98.819 3152 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.91 % Allowed : 20.03 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2608 helix: 0.31 (0.13), residues: 1512 sheet: -3.14 (0.44), residues: 108 loop : -1.45 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 481 HIS 0.002 0.000 HIS B 523 PHE 0.033 0.001 PHE D 590 TYR 0.018 0.001 TYR B 451 ARG 0.005 0.000 ARG D 487 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4358.41 seconds wall clock time: 78 minutes 39.51 seconds (4719.51 seconds total)